The objective of this work is to evaluate the concentration of cyanogenic glycosides CGs (amygdalin and prunasin) in the cultivar and rootstock, as an indicator of compatibility in pear grafts. The work consists of two experiments. Experiment 1 evaluated Cascatense/Pyrus Calleryana and Cascatense/EMC combinations. Experiment 2 evaluated the combinations Packham’s Triumph/Adams, Santa Maria/Adams, and Rocha/Adams. The experimental design of the two experiments was randomized blocks with four replications. The evaluations were carried out in the spring and summer of the harvest 2014/2015. The results indicated graft compatibility in the Cascatense/P. Calleryana, Packham’s Triumph/Adams, and Rocha/Adams combinations; slight incompatibility of Santa Maria/Adams, and severe incompatibility of Cascatense/EMC. The obtained results indicate that differences ≥ 20 mg g-1 of CGs between scion and rootstock were correlated with a drastic reduction in vigor, problems of continuity in graft union, low yield, and early defoliation.